Sounds like you may be expecting Captivate to work
identically to Flash. Sorry my friend, it doesn't work this way.
For starters, notice that Captivate uses slides.
Each slide has its own timeline. So what you see in the timeline
area is not for the whole movie.
As you add objects (Buttons, Click Boxes, Images, Rollover
Areas, Etc.) the object is placed on the timeline and assumes what
you are referring to as a layer. You then control which object is
in front of another object by its relative position in the layer.
This is called the "Stacking Order".